Fig 2: Knockdown of RBM17, U2SURP, or CHERP Alters Expression of RNA-Processing Factors(A) Plot showing the overlap pattern of differentially expressed genes across the knockdown models of RBM17, U2SURP, or CHERP (n = 3 replicates/siRNA, including siScramble). The red and blue bars represent all genes common to the three datasets (from the three interacting proteins)and consistently altered in the same direction: downregulated (red) and upregulated (blue). The black dots beneath the x axis indicate which proteins have been knocked down for each dataset and the direction of the resulting gene expression changes. The percentages at the top of the graph describe the size of the group of overlapping changes relatively to the biggest and the smallest of the three datasets.(B) Validation of selected gene expression changes by qRT-PCR. The levels of selected transcripts were measured using qRT-PCR on samples from HEK293T cells treated with siRBM17, siU2SURP, or siCHERP and compared to cells treated with siScramble (n = 4 replicates/siRNA run in technical triplicates). Bars represent mean ± SEM; p value was calculated by two-tailed Student’s t test and significance was set at p < 0.05.(C) Network plot of functionally enriched categories in overlapping differentially expressed genes. Each node is a functional category. The width of the connector between nodes is directly proportional to the number of genes shared between respective categories.See also Tables S2 and S3.

Fig 3: RBM17, SF3B1, U2SURP, and CHERP Interact with One Another and Regulate Reciprocal Protein Stability(A–C) Representative western blots (left) and protein-level quantifications (right) of SF3B1, U2SURP, CHERP, and RBM17 in HEK293T cells treated with siSF3B1 (A), siU2SURP (B), or siCHERP (C) and compared to cells treated with control siScramble (n = 6–18 replicates/siRNA). All data were normalized to VCL, used here as loading control. Bars represent mean ± SEM; p value was calculated by two-tailed Student’s t test, and significance was set at p < 0.05. The presence of a dashed line between Scramble and siRNA samples indicates that the image of the membrane has been modified to eliminate a marker lane between the two sets of samples. See also Figures S3 and S4.

Fig 4: The Molecular Signature of the Functional Unit Formed by RBM17, U2SURP, and CHERP Is Specific(A) Overlap of gene expression changes across cells treated with shRNA against RBM17, RBM22, or PRPF8 in K562 cells. The red and blue bars represent all genes common to the three datasets and consistently altered in the same direction: downregulated (red) or upregulated (blue).(B) Number of exclusion and inclusion splicing events relative to the five categories of AS evaluated by rMATS and caused by RNAi of RBM17, RBM22, or PRPF8 in K562 cells. The fourth column describes the size of the list of shared events across the three conditions.(C) Overlap of gene expression changes across cells treated with shRNA against RBM17, U2AF1, or U2AF2 in K562 cells. The red and blue bars represent all genes common to the three datasets and consistently altered in the same direction: downregulated (red) or upregulated (blue).(D) Number of exclusion and inclusion splicing events relative to the five categories of AS evaluated by rMATS and caused by RNAi of RBM17, U2AF1, or U2AF2. The fourth column describes the size of the list of shared events across the three conditions.Each of the ENCODE RNA sequencing datasets we reanalyzed has n = 2 replicates/shRNA. SE, skipped exons; A5SS, alternative 5' splice site; A3SS, alternative 3' splice site; MXE, mutually exclusive exons; RI, retained introns.